MHCtools: Analysis of MHC Data in Non-Model Species

Ten tools for analysis of major histocompatibility complex (MHC) data in non-
model species. The functions are tailored for amplicon data sets that have been
filtered using the 'dada2' method (for more information visit
<https://benjjneb.github.io/dada2>), but even other data sets can be analysed,
if the data tables are formatted according to the description in each function.
The ReplMatch() function matches replicates in data sets in order to evaluate
genotyping success.
The GetReplTable() and GetReplStats() functions perform such an evaluation.
The HpltFind() function infers putative haplotypes from families in the data
set.
The GetHpltTable() and GetHpltStats() functions evaluate the accuracy of
the haplotype inference.
The PapaDiv() function compares parent pairs in the data set and calculate their
joint MHC diversity, taking into account sequence variants that occur in both
parents.
The MeanPdist() function calculates the mean p-distance from pairwise
comparisons sequences in each sample in a data set. The function includes the
option to specify which codons to compare.
The CreateFas() function creates a fasta file with all the sequences in the data
set.
The CreateSamplesFas() function creates a fasta file for each sample in the data
set.